tag_sequenceExperiment: Extracts read sequences

In cancer-genomics/trellis: Somatic structural variant analysis

Extracts read sequences

Description

This function extracts the sequences of reads from a bam file and saves the result as an interemediate file. If the intermediate file already exists, the read sequences are read from disk.

Usage

tag_sequenceExperiment(dp, rlist, aviews, MAX = 25L)

Arguments

dp	a DataPaths object
rlist	a RearrangementList
aviews	an AlignmentViews2 object
MAX	the maximum number of read pairs to extract for a rearrangement. If the number of read pairs supporting a rearrangement is greater than MAX, a random sample of MAX supporting read pairs is returned.

Details

This function calls getReadAlignmentPairs, the function originally called by writeImproperAlignments2. The reason we call this function a second time is that the read sequences were not saved in the initial query. Saving the sequences in the original query would prevent having to access the bam file a second time, though increase the size of the improper read files. We could use. Another improvement in efficiency might come from parsing the original large bam into a smaller bam containing improper read pairs in which both mates were mapped.

cancer-genomics/trellis documentation built on Feb. 2, 2023, 7:04 p.m.